In certain situations, it may be desirable to inhibit the function of RNA and regulate its expression. For example, one method of treating bacterial or viral infections involves inhibiting the expression of bacterial or viral mRNA. Another method involves interfering with the ability of ribosomal RNA to take part in the mechanics of bacterial protein synthesis.
Certain classes of antibiotics are known to interact with RNA. For example, the antibiotic thiostreptone binds tightly to a 60mer from ribosomal RNA (Cundliffe et al., in The Ribosome: Structure, Function & Evolution (Schlessinger et al., eds.) American Society for Microbiology, Washington, D.C. (1990) pp. 479-490). Resistance to various antibiotics often involves methylation at specific rRNA sites (Cundliffe (1989) Ann. Rev. Microbiol. 43: 207-233). Aminoglycosidic aminocyclitol (aminoglycoside) antibiotics and peptide antibiotics are known to inhibit group I intron splicing by binding to specific regions of the RNA (von Ahsen et al. (1991) Nature (London) 353: 368-370). Some of these same aminoglycosides have also been found to inhibit hammerhead ribozyme function (Stage et al. (1995) RNA 1: 95-101). In addition, certain aminoglycosides and other protein synthesis inhibitors have been found to interact with specific bases in 16S rRNA (Woodcock et al. (1991) EMBO J. 10: 3099-3103). An oligonucleotide analog of the 16S rRNA has also been shown to interact with certain aminoglycosides (Purohit et al. (1994) Nature 370: 659-662). A molecular basis for hypersensitivity to aminoglycosides has been found to be located in a single base change in mitochondrial rRNA (Hutchin et al. (1993) Nucleic Acids Res. 21: 4174-4179).
While these findings implicate RNA as the target for various antibiotics, there are few if any quantitative reports of the specific binding of any aminoglycoside directly to a particular domain of an RNA molecule.
Zapp et al. (Cell (1993) 74: 969-978) has demonstrated that neomycin B, lividomycin A, and tobramycin can block the binding of Rev, a viral regulatory protein required for viral gene expression, to its viral recognition element in the IIB (or RRE) region of HIV RNA. This blockage appears to be the result of competitive binding of the antibiotics to the RNA.
Thus, there is a need to elucidate the nature of the specific interaction between antibiotics and RNA which results in the inhibition of RNA function. There also remains a need for new antibiotics as well as other compounds which can effectively inhibit the function of specific RNAs with greater specificity and/or potency than existing antibiotics or compounds. A need for efficient methods of identifying these new compounds also exists.